global.R

# Deer-vehicle collisions in Scotland, 2000 to 2017: a Shiny app
# Data preparation
# Jan 2018
# Matt Dray

# Load packages -----------------------------------------------------------


# Data manipulation and cleaning
library(dplyr)  # tidy data manipulation
library(stringr)  # string manipulation
library(janitor)  # misc tidy data manipulation
library(lubridate)  # dealing with dates and times
library(forcats)  # deal with factors
library(sf)  # geography
library(flexdashboard)  # layout of the tool (pages, frames, etc)
library(crosstalk)  # for allowing htmlwidgets to interact with shared data
library(leaflet)  # interactive maps
library(DT)  # interactive tables


# Read and wrangle data ---------------------------------------------------


dvc_read <- st_read(  # read geographic data
  "data/DVC_SCOTLAND_ESRI/DVC_SCOTLAND.shp",  # shapefile stored in repo
  stringsAsFactors = FALSE  # read factor columns as character columns
) 

dvc_wrangle <- dvc_read %>% 
  st_transform(crs = 4326) %>%  # transform coords to latlong
  # decapitalise everything for easy handling
  rename_all(tolower) %>% 
  mutate_if(is.character, tolower) %>%  # simplify strings
  # deal with dates
  mutate(
    inc_date = ymd(inc_date),
    inc_month = case_when(
      inc_month == 1 ~  "Jan", inc_month == 2 ~  "Feb",
      inc_month == 3 ~  "Mar", inc_month == 4 ~  "Apr",
      inc_month == 5 ~  "May", inc_month == 6 ~  "Jun",
      inc_month == 7 ~  "Jul", inc_month == 8 ~  "Aug",
      inc_month == 9 ~  "Sep", inc_month == 10 ~ "Oct",
      inc_month == 11 ~ "Nov", inc_month == 12 ~ "Dec",
      TRUE ~ "Unknown"
    ),
    # clean up strings (not perfect)
    deer_speci = if_else(deer_speci %in% c("desppnk", "uncl.", "nk"), "unknown", deer_speci),
    localautho = if_else(localautho == "perth & kinross", "perth_and_kinross", localautho),
    road_no = if_else(str_detect(road_no, "x") == TRUE, "unknown", road_no),
    road_no = if_else(
      road_no %in% c(
        "unknown", "nk", "unalloc", "notallocated", "notalloc", "unclassified",
        "new", "other",  "a", "b", "c", "u", "aps", "arnl", "uncl", "no",
        "causeymount", "rdporthleven", "kirkinkillochtokilsyth", "grandholmroad",
        "largoroad" 
      ), "unknown", road_no
    ),
    # final name tidy-up
    localautho = str_replace_all(localautho, "_", " ")
  ) %>% 
  # title case for these columns
  mutate_at(vars(deer_speci, localautho, road_no), tools::toTitleCase) # To Title Case

# extract latlong cols from sf geometry and bind back to df
dvc_xy <- as.data.frame(st_coordinates(dvc_wrangle))
dvc <- bind_cols(dvc_wrangle, dvc_xy) %>% rename(latitude = X, longitude = Y)


# Sample ------------------------------------------------------------------


# create sample for testing the app (50 per year)
# dvc_sample <- dvc %>% 
#   group_by(year) %>%  # within each year
#   sample_n(50)  # random selection


# Shared data -------------------------------------------------------------


# create shared data object for crosstalk
# dvc_sd <- SharedData$new(dvc)
# dvc_sd <- SharedData$new(dvc_sample)


# Save objects ------------------------------------------------------------


saveRDS(dvc, "data/dvc.RDS")
write.csv(dvc, "data/dvc.csv")
# saveRDS(dvc_sample, "data/dvc_sample.RDS")